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Highly abundant proteins favor more stable 3D structures in yeast.

ABSTRACT: To understand the variation of protein sequences in nature, we need to reckon with evolutionary constraints that are biophysical, cellular, and ecological. Here, we show that under the global selection against protein misfolding, there exists a scaling among protein folding stability, protein cellular abundance, and effective population size. The specific scaling implies that the several-orders-of-magnitude range of protein abundances in the cell should leave imprints on extant protein structures, a prediction that is supported by our structural analysis of the yeast proteome.

SUBMITTER: Serohijos AW

PROVIDER: S-EPMC3566449 | biostudies-other | 2013 Feb

REPOSITORIES: biostudies-other

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Highly abundant proteins favor more stable 3D structures in yeast.

Serohijos Adrian W R AW Lee S Y Ryan SY Shakhnovich Eugene I EI

Biophysical journal 20130201 3

To understand the variation of protein sequences in nature, we need to reckon with evolutionary constraints that are biophysical, cellular, and ecological. Here, we show that under the global selection against protein misfolding, there exists a scaling among protein folding stability, protein cellular abundance, and effective population size. The specific scaling implies that the several-orders-of-magnitude range of protein abundances in the cell should leave imprints on extant protein structure ...[more]

PMID: 23442924

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Project description:BackgroundWhile many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown.ResultsUsing next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation.ConclusionsGiven log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.

Project description:Yeast filamentous growth is a stress response to conditions of nitrogen deprivation, wherein yeast colonies form pseudohyphal filaments of elongated and connected cells. As proteins mediating adhesion and transport are required for this growth transition, we expect that the protein complement at the yeast cell periphery plays a critical and tightly regulated role in pseudohyphal filamentation. To identify proteins differentially abundant at the yeast cell periphery during pseudohyphal growth, we generated quantitative proteomic profiles of plasma membrane protein preparations under conditions of vegetative growth and filamentation. By isobaric tags for relative and absolute quantification chemistry and two-dimensional liquid chromatography-tandem mass spectrometry, we profiled 2463 peptides and 356 proteins, identifying 11 differentially abundant proteins that localize to the yeast cell periphery. This protein set includes Ylr414cp, herein renamed Pun1p, a previously uncharacterized protein localized to the plasma membrane compartment of Can1. Pun1p abundance is doubled under conditions of nitrogen stress, and deletion of PUN1 abolishes filamentous growth in haploids and diploids; pun1Delta mutants are noninvasive, lack surface-spread filamentation, grow slowly, and exhibit impaired cell adhesion. Conversely, overexpression of PUN1 results in exaggerated cell elongation under conditions of nitrogen stress. PUN1 contributes to yeast nitrogen signaling, as pun1Delta mutants misregulate amino acid biosynthetic genes during nitrogen stress. By chromatin immunoprecipitation and reverse transcription-PCR, we find that the filamentous growth factor Mss11p directly binds the PUN1 promoter and regulates its transcription. In total, this study provides the first profile of differential protein abundance during pseudohyphal growth, identifying a previously uncharacterized membrane compartment of Can1 protein required for wild-type nitrogen signaling and filamentous growth.

Project description:Electrochemical stability of energy storage devices is one of their major concerns. Polymeric binders are generally used to enhance the stability of the electrode, but the electrochemical performance of the device is compromised due to the poor conductivity of the binders. Herein, 3D binder-free electrode based on nickel oxide deposited on graphene (G-NiO) was fabricated by a simple two-step method. First, graphene was deposited on nickel foam via atmospheric pressure chemical vapour deposition followed by electrodeposition of NiO. The structural and morphological analyses of the fabricated G-NiO electrode were conducted through Raman spectroscopy, X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), and energy dispersive X-ray spectroscopy (EDS). XRD and Raman results confirmed the successful growth of high-quality graphene on nickel foam. FESEM images revealed the sheet and urchin-like morphology of the graphene and NiO, respectively. The electrochemical performance of the fabricated electrode was evaluated through cyclic voltammetry (CV), galvanostatic charge-discharge (GCD), and electrochemical impedance spectroscopy (EIS) in aqueous solution at room temperature. The G-NiO binder-free electrode exhibited a specific capacity of ? 243 C g-1 at 3 mV s-1 in a three-electrode cell. A two-electrode configuration of G-NiO//activated charcoal was fabricated to form a hybrid device (supercapattery) that operated in a stable potential window of 1.4 V. The energy density and power density of the asymmetric device measured at a current density of 0.2 A g-1 were estimated to be 47.3 W h kg-1 and 140 W kg-1, respectively. Additionally, the fabricated supercapattery showed high cyclic stability with 98.7% retention of specific capacity after 5,000 cycles. Thus, the proposed fabrication technique is highly suitable for large scale production of highly stable and binder-free electrodes for electrochemical energy storage devices.

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Highly abundant proteins favor more stable 3D structures in yeast.

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Highly abundant proteins favor more stable 3D structures in yeast.

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